7-155057913-C-T

Variant names:

• chr7-155057913-C-T
• rs1440461

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 0.55 in 151,928 control chromosomes in the GnomAD database, including 23,930 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 0.55 (23930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 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: 0.550 AC: 83525 AN: 151810 Hom.: 23923 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.550 AC: 83544 AN: 151928 Hom.: 23930 Cov.: 31 AF XY: 0.545 AC XY: 40488 AN XY: 74244

African (AFR) AF: 0.387 AC: 16024 AN: 41416

American (AMR) AF: 0.622 AC: 9493 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2232 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2124 AN: 5150

South Asian (SAS) AF: 0.554 AC: 2668 AN: 4812

European-Finnish (FIN) AF: 0.537 AC: 5656 AN: 10538

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43446 AN: 67956

Other (OTH) AF: 0.563 AC: 1188 AN: 2112

Alfa AF: 0.597 Hom.: 46974

Bravo AF: 0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1440461; hg19: chr7-154849623;