chr7-149506571-A-C

Variant names:

• chr7-149506571-A-C
• rs855913

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 0.962 in 152,292 control chromosomes in the GnomAD database, including 70,568 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 0.96 (70568 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 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: 0.962 AC: 146447 AN: 152174 Hom.: 70508 Cov.: 31

Gnomad AFR AF: 0.990

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.962

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

GnomAD4 genome AF: 0.962 AC: 146566 AN: 152292 Hom.: 70568 Cov.: 31 AF XY: 0.964 AC XY: 71789 AN XY: 74470

African (AFR) AF: 0.990 AC: 41133 AN: 41554

American (AMR) AF: 0.974 AC: 14900 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3288 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5186

South Asian (SAS) AF: 0.996 AC: 4803 AN: 4820

European-Finnish (FIN) AF: 0.955 AC: 10134 AN: 10610

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63962 AN: 68036

Other (OTH) AF: 0.962 AC: 2034 AN: 2114

Alfa AF: 0.945 Hom.: 239771

Bravo AF: 0.964

Asia WGS AF: 0.995 AC: 3462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.49
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs855913; hg19: chr7-149203662;