rs62471956

Positions:

• chr7-99823462-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0331 in 152,152 control chromosomes in the GnomAD database, including 107 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 0.033 (107 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0331 (5040/152152) while in subpopulation NFE AF= 0.0497 (3376/67980). AF 95% confidence interval is 0.0483. There are 107 homozygotes in gnomad4. There are 2472 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 107 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 5039 AN: 152032 Hom.: 107 Cov.: 31

Gnomad AFR AF: 0.00882

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00912

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0331 AC: 5040 AN: 152152 Hom.: 107 Cov.: 31 AF XY: 0.0332 AC XY: 2472 AN XY: 74380

Gnomad4 AFR AF: 0.00879

Gnomad4 AMR AF: 0.0247

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00913

Gnomad4 FIN AF: 0.0501

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0379 Hom.: 16

Bravo AF: 0.0308

Asia WGS AF: 0.00693 AC: 24 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	4.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62471956; hg19: chr7-99421085;