rs4716990

Variant names:

• chr7-156131242-A-G
• rs4716990

Your query was ambiguous. Multiple possible variants found:

• chr7-156131242-A-G
• chr7-156131242-A-T

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 0.355 in 151,954 control chromosomes in the GnomAD database, including 10,278 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 0.35 (10278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 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: 0.355 AC: 53882 AN: 151834 Hom.: 10281 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.355 AC: 53899 AN: 151954 Hom.: 10278 Cov.: 32 AF XY: 0.357 AC XY: 26504 AN XY: 74302

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.378

Alfa AF: 0.318 Hom.: 3738

Bravo AF: 0.371

Asia WGS AF: 0.399 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4716990; hg19: chr7-155923936;