rs1105305

Variant names:

• chr7-56573692-A-C
• rs1105305

Your query was ambiguous. Multiple possible variants found:

• chr7-56573692-A-C
• chr7-56573692-A-T

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 0.307 in 152,154 control chromosomes in the GnomAD database, including 7,772 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 0.31 (7772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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: 0.307 AC: 46749 AN: 152036 Hom.: 7764 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.00827

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.307 AC: 46778 AN: 152154 Hom.: 7772 Cov.: 32 AF XY: 0.303 AC XY: 22558 AN XY: 74398

African (AFR) AF: 0.428 AC: 17738 AN: 41482

American (AMR) AF: 0.277 AC: 4239 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3470

East Asian (EAS) AF: 0.00791 AC: 41 AN: 5186

South Asian (SAS) AF: 0.199 AC: 958 AN: 4818

European-Finnish (FIN) AF: 0.264 AC: 2791 AN: 10588

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19215 AN: 68002

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.253 Hom.: 1785

Bravo AF: 0.313

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1105305; hg19: chr7-56641385;