16-254804-A-T

Variant names:

• chr16-254804-A-T
• rs7189020
• NM_032039.4:c.268+123A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032039.4(FAM234A):​c.268+123A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 976,930 control chromosomes in the GnomAD database, including 106,169 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.54 (25890 hom., cov: 32)
  • Exomes 𝑓: 0.43 (80279 hom.)
• Consequence: FAM234A NM_032039.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.57
• Publications: 24 publications found

Genes affected

FAM234A (HGNC:14163): (family with sequence similarity 234 member A) Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032039.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM234A	NM_032039.4	MANE Select	c.268+123A>T		intron	N/A	NP_114428.1
	FAM234A	NM_001284497.2		c.268+123A>T		intron	N/A	NP_001271426.1
	FAM234A	NR_104317.2		n.444+123A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM234A	ENST00000399932.8	TSL:1 MANE Select	c.268+123A>T		intron	N/A	ENSP00000382814.3
	FAM234A	ENST00000301678.7	TSL:1	c.268+123A>T		intron	N/A	ENSP00000301678.3
	FAM234A	ENST00000301679.7	TSL:2	c.268+123A>T		intron	N/A	ENSP00000301679.2

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82427 AN: 152002 Hom.: 25823 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.427 AC: 352434 AN: 824810 Hom.: 80279 AF XY: 0.428 AC XY: 180861 AN XY: 422530

African (AFR) AF: 0.879 AC: 17535 AN: 19958

American (AMR) AF: 0.570 AC: 15754 AN: 27632

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 8055 AN: 16804

East Asian (EAS) AF: 0.638 AC: 23205 AN: 36390

South Asian (SAS) AF: 0.514 AC: 30041 AN: 58444

European-Finnish (FIN) AF: 0.300 AC: 11399 AN: 37966

Middle Eastern (MID) AF: 0.538 AC: 1436 AN: 2668

European-Non Finnish (NFE) AF: 0.388 AC: 227481 AN: 586210

Other (OTH) AF: 0.452 AC: 17528 AN: 38738

GnomAD4 genome AF: 0.543 AC: 82560 AN: 152120 Hom.: 25890 Cov.: 32 AF XY: 0.537 AC XY: 39899 AN XY: 74334

African (AFR) AF: 0.865 AC: 35909 AN: 41528

American (AMR) AF: 0.514 AC: 7864 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3466

East Asian (EAS) AF: 0.641 AC: 3317 AN: 5172

South Asian (SAS) AF: 0.520 AC: 2507 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3018 AN: 10574

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26592 AN: 67952

Other (OTH) AF: 0.538 AC: 1136 AN: 2110

Alfa AF: 0.465 Hom.: 2211

Bravo AF: 0.578

Asia WGS AF: 0.617 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.36
PhyloP100		-3.6
PromoterAI		0.033	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7189020; hg19: chr16-304803;