rs6498937

Variant names:

• chr16-64174077-C-A
• rs6498937
• ENST00000722564.1:n.61-2608C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-64174077-C-A
• chr16-64174077-C-T

Variant summary

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

The ENST00000722564.1(ENSG00000294295):​n.61-2608C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,962 control chromosomes in the GnomAD database, including 6,323 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 0.21 (6323 hom., cov: 32)
• Consequence: ENSG00000294295 ENST00000722564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 1 publications found

Genes affected

ENSG00000294295 (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 = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294295	ENST00000722564.1	n.61-2608C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32084 AN: 151844 Hom.: 6313 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.211 AC: 32139 AN: 151962 Hom.: 6323 Cov.: 32 AF XY: 0.210 AC XY: 15602 AN XY: 74296

African (AFR) AF: 0.511 AC: 21127 AN: 41384

American (AMR) AF: 0.195 AC: 2969 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1421 AN: 5156

South Asian (SAS) AF: 0.177 AC: 850 AN: 4810

European-Finnish (FIN) AF: 0.0356 AC: 377 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0672 AC: 4567 AN: 67996

Other (OTH) AF: 0.173 AC: 365 AN: 2114

Alfa AF: 0.115 Hom.: 6773

Bravo AF: 0.239

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.34
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs6498937; hg19: chr16-64207981;