rs237131

Variant names:

• chr16-26629085-G-A
• rs237131
• ENST00000806412.1:n.67-12720G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-26629085-G-A
• chr16-26629085-G-C

Variant summary

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

The ENST00000806412.1(ENSG00000304809):​n.67-12720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,128 control chromosomes in the GnomAD database, including 7,500 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 0.30 (7500 hom., cov: 32)
• Consequence: ENSG00000304809 ENST00000806412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 6 publications found

Genes affected

ENSG00000304809 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806412.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304809	ENST00000806412.1		n.67-12720G>A		intron	N/A
	ENSG00000304829	ENST00000806514.1		n.267-6782C>T		intron	N/A
	ENSG00000304829	ENST00000806515.1		n.71-6782C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45022 AN: 152010 Hom.: 7504 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.296 AC: 45022 AN: 152128 Hom.: 7500 Cov.: 32 AF XY: 0.292 AC XY: 21675 AN XY: 74354

African (AFR) AF: 0.134 AC: 5575 AN: 41522

American (AMR) AF: 0.340 AC: 5196 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1383 AN: 3472

East Asian (EAS) AF: 0.478 AC: 2467 AN: 5164

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4822

European-Finnish (FIN) AF: 0.292 AC: 3086 AN: 10574

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25171 AN: 67968

Other (OTH) AF: 0.336 AC: 708 AN: 2108

Alfa AF: 0.351 Hom.: 42481

Bravo AF: 0.298

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.40
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs237131; hg19: chr16-26640406;