rs6499500

Variant names:

• chr16-71314512-C-G
• rs6499500
• ENST00000727102.1:n.362-13208G>C

Your query was ambiguous. Multiple possible variants found:

• chr16-71314512-C-G
• chr16-71314512-C-T

Variant summary

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

The ENST00000727102.1(ENSG00000294967):​n.362-13208G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,058 control chromosomes in the GnomAD database, including 34,169 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 0.65 (34169 hom., cov: 32)
• Consequence: ENSG00000294967 ENST00000727102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 6 publications found

Genes affected

ENSG00000294967 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727102.1. 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
	ENSG00000294967	ENST00000727102.1		n.362-13208G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99263 AN: 151940 Hom.: 34109 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.654 AC: 99388 AN: 152058 Hom.: 34169 Cov.: 32 AF XY: 0.650 AC XY: 48313 AN XY: 74312

African (AFR) AF: 0.877 AC: 36417 AN: 41512

American (AMR) AF: 0.669 AC: 10227 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3464

East Asian (EAS) AF: 0.635 AC: 3268 AN: 5150

South Asian (SAS) AF: 0.576 AC: 2777 AN: 4820

European-Finnish (FIN) AF: 0.486 AC: 5121 AN: 10544

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37297 AN: 67974

Other (OTH) AF: 0.634 AC: 1339 AN: 2112

Alfa AF: 0.480 Hom.: 1359

Bravo AF: 0.681

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.74
DANN	Benign	0.76
PhyloP100		-0.89

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6499500;

hg19: chr16-71348415;