6-13514065-A-G

Variant names:

• chr6-13514065-A-G
• rs4715377

Variant summary

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

The variant allele was found at a frequency of 0.0604 in 152,250 control chromosomes in the GnomAD database, including 405 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 0.060 (405 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0891 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

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9201 AN: 152132 Hom.: 405 Cov.: 33

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0518

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0220

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0910

Gnomad OTH AF: 0.0697

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

GnomAD4 genome AF: 0.0604 AC: 9200 AN: 152250 Hom.: 405 Cov.: 33 AF XY: 0.0584 AC XY: 4343 AN XY: 74426

African (AFR) AF: 0.0161 AC: 669 AN: 41554

American (AMR) AF: 0.0670 AC: 1025 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0518 AC: 180 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4818

European-Finnish (FIN) AF: 0.0650 AC: 690 AN: 10610

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0909 AC: 6185 AN: 68006

Other (OTH) AF: 0.0690 AC: 146 AN: 2116

Alfa AF: 0.0707 Hom.: 302

Bravo AF: 0.0595

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.71
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4715377; hg19: chr6-13514297;