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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0615

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.177

Alfa AF: 0.190 Hom.: 4790

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs715987; hg19: chr10-4598903;