rs1474554

Variant names:

• chr6-170529763-T-C
• rs1474554

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 0.46 in 146,604 control chromosomes in the GnomAD database, including 15,673 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 0.46 (15673 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 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: 0.460 AC: 67377 AN: 146494 Hom.: 15662 Cov.: 25

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.460 AC: 67410 AN: 146604 Hom.: 15673 Cov.: 25 AF XY: 0.463 AC XY: 32976 AN XY: 71234

African (AFR) AF: 0.357 AC: 14172 AN: 39726

American (AMR) AF: 0.540 AC: 7945 AN: 14704

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1741 AN: 3426

East Asian (EAS) AF: 0.243 AC: 1077 AN: 4436

South Asian (SAS) AF: 0.543 AC: 2425 AN: 4466

European-Finnish (FIN) AF: 0.528 AC: 5110 AN: 9678

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 33553 AN: 66942

Other (OTH) AF: 0.462 AC: 948 AN: 2052

Alfa AF: 0.465 Hom.: 2169

Bravo AF: 0.441

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1474554; hg19: chr6-170838851;