rs715987

Variant names:

• chr10-4556711-T-C
• rs715987

Your query was ambiguous. Multiple possible variants found:

• chr10-4556711-T-C
• chr10-4556711-T-G

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 0.16 in 152,004 control chromosomes in the GnomAD database, including 2,367 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 0.16 (2367 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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: 0.160 AC: 24361 AN: 151890 Hom.: 2366 Cov.: 30

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.160 AC: 24369 AN: 152004 Hom.: 2367 Cov.: 30 AF XY: 0.163 AC XY: 12118 AN XY: 74308

African (AFR) AF: 0.0615 AC: 2550 AN: 41488

American (AMR) AF: 0.148 AC: 2254 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3472

East Asian (EAS) AF: 0.157 AC: 812 AN: 5174

South Asian (SAS) AF: 0.134 AC: 644 AN: 4814

European-Finnish (FIN) AF: 0.295 AC: 3100 AN: 10524

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.200 AC: 13587 AN: 67954

Other (OTH) AF: 0.177 AC: 372 AN: 2106

Alfa AF: 0.180 Hom.: 7127

Bravo AF: 0.143

Asia WGS AF: 0.142 AC: 496 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.89
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs715987; hg19: chr10-4598903;