chr16-1943476-A-G

Variant names:

• chr16-1943476-A-G
• rs732510
• XR_007064940.1:n.580A>G

Variant summary

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

The XR_007064940.1(LOC124903625):​n.580A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 379,058 control chromosomes in the GnomAD database, including 59,731 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 0.58 (28400 hom., cov: 32)
  • Exomes 𝑓: 0.50 (31331 hom.)
• Consequence: LOC124903625 XR_007064940.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 6 publications found

Genes affected

LOC124903625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728751.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295233	ENST00000728751.1		n.-9A>G		upstream_gene	N/A
	ENSG00000295233	ENST00000728752.1		n.-13A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88168 AN: 151804 Hom.: 28341 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.539

GnomAD4 exome AF: 0.501 AC: 113761 AN: 227138 Hom.: 31331 AF XY: 0.525 AC XY: 64069 AN XY: 122028

African (AFR) AF: 0.854 AC: 4094 AN: 4794

American (AMR) AF: 0.427 AC: 3577 AN: 8374

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 3264 AN: 6260

East Asian (EAS) AF: 0.669 AC: 8026 AN: 11998

South Asian (SAS) AF: 0.775 AC: 26044 AN: 33598

European-Finnish (FIN) AF: 0.443 AC: 5782 AN: 13042

Middle Eastern (MID) AF: 0.504 AC: 453 AN: 898

European-Non Finnish (NFE) AF: 0.416 AC: 56436 AN: 135568

Other (OTH) AF: 0.483 AC: 6085 AN: 12606

GnomAD4 genome AF: 0.581 AC: 88279 AN: 151920 Hom.: 28400 Cov.: 32 AF XY: 0.587 AC XY: 43603 AN XY: 74252

African (AFR) AF: 0.859 AC: 35609 AN: 41474

American (AMR) AF: 0.483 AC: 7365 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1891 AN: 3464

East Asian (EAS) AF: 0.656 AC: 3352 AN: 5112

South Asian (SAS) AF: 0.795 AC: 3835 AN: 4826

European-Finnish (FIN) AF: 0.471 AC: 4987 AN: 10586

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29482 AN: 67886

Other (OTH) AF: 0.544 AC: 1147 AN: 2108

Alfa AF: 0.523 Hom.: 4537

Bravo AF: 0.582

Asia WGS AF: 0.727 AC: 2528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		-1.5
PromoterAI		-0.14	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs732510; hg19: chr16-1993477;