rs1122794

Variant names:

• chr16-259156-C-A
• rs1122794
• NM_032039.4:c.269-327C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-259156-C-A
• chr16-259156-C-G
• chr16-259156-C-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.269-327C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,080 control chromosomes in the GnomAD database, including 2,913 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 0.19 (2913 hom., cov: 32)
• Consequence: FAM234A NM_032039.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 27 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM234A	NM_032039.4	c.269-327C>A		intron_variant	Intron 3 of 12	ENST00000399932.8	NP_114428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM234A	ENST00000399932.8	c.269-327C>A		intron_variant	Intron 3 of 12	1	NM_032039.4	ENSP00000382814.3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29284 AN: 151962 Hom.: 2909 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.198

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.193 AC: 29307 AN: 152080 Hom.: 2913 Cov.: 32 AF XY: 0.192 AC XY: 14283 AN XY: 74338

African (AFR) AF: 0.194 AC: 8058 AN: 41482

American (AMR) AF: 0.214 AC: 3273 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3470

East Asian (EAS) AF: 0.149 AC: 769 AN: 5162

South Asian (SAS) AF: 0.274 AC: 1319 AN: 4818

European-Finnish (FIN) AF: 0.166 AC: 1755 AN: 10586

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12718 AN: 67978

Other (OTH) AF: 0.199 AC: 420 AN: 2108

Alfa AF: 0.189 Hom.: 5749

Bravo AF: 0.196

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.67
PhyloP100		0.057
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: rs1122794; hg19: chr16-309155;