rs1443711

Variant names:

• chr2-31171810-A-G
• rs1443711

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 0.208 in 152,246 control chromosomes in the GnomAD database, including 4,101 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 0.21 (4101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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: 0.208 AC: 31635 AN: 152128 Hom.: 4101 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.208 AC: 31628 AN: 152246 Hom.: 4101 Cov.: 32 AF XY: 0.203 AC XY: 15135 AN XY: 74428

African (AFR) AF: 0.0747 AC: 3106 AN: 41570

American (AMR) AF: 0.206 AC: 3157 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3468

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5190

South Asian (SAS) AF: 0.129 AC: 624 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2617 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20406 AN: 67998

Other (OTH) AF: 0.228 AC: 483 AN: 2116

Alfa AF: 0.270 Hom.: 3704

Bravo AF: 0.198

Asia WGS AF: 0.0640 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.52
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1443711; hg19: chr2-31394676;