rs56036015

Variant names:

• chr6-31575287-A-C
• rs56036015

Your query was ambiguous. Multiple possible variants found:

• chr6-31575287-A-C
• chr6-31575287-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant allele was found at a frequency of 0.00000306 in 326,714 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000031 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 5 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD2 exomes AF: 0.00000695 AC: 1 AN: 143782 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000170

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000306 AC: 1 AN: 326714 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 184980

African (AFR) AF: 0.00 AC: 0 AN: 9538

American (AMR) AF: 0.00 AC: 0 AN: 28340

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11552

East Asian (EAS) AF: 0.00 AC: 0 AN: 10870

South Asian (SAS) AF: 0.00 AC: 0 AN: 60050

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14200

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2852

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 173614

Other (OTH) AF: 0.0000637 AC: 1 AN: 15698

GnomAD4 genome Cov.: 31

Alfa AF: 0.0000434 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		0.023
PromoterAI		-0.027	Neutral

Splicing

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

Other links and lift over

dbSNP: rs56036015; hg19: chr6-31543064;