rs488966

Variant names:

• chr6-153962733-T-C
• rs488966

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.7 in 152,088 control chromosomes in the GnomAD database, including 37,547 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 0.70 (37547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 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: 0.701 AC: 106460 AN: 151972 Hom.: 37543 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.700 AC: 106500 AN: 152088 Hom.: 37547 Cov.: 32 AF XY: 0.705 AC XY: 52409 AN XY: 74348

African (AFR) AF: 0.671 AC: 27799 AN: 41460

American (AMR) AF: 0.666 AC: 10176 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2170 AN: 3470

East Asian (EAS) AF: 0.755 AC: 3898 AN: 5162

South Asian (SAS) AF: 0.765 AC: 3685 AN: 4820

European-Finnish (FIN) AF: 0.792 AC: 8375 AN: 10570

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48089 AN: 68004

Other (OTH) AF: 0.666 AC: 1403 AN: 2106

Alfa AF: 0.692 Hom.: 13021

Bravo AF: 0.689

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	18
DANN	Benign	0.70
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs488966; hg19: chr6-154283868;