rs1949891

Variant names:

• chr13-84815953-G-A
• rs1949891

Your query was ambiguous. Multiple possible variants found:

• chr13-84815953-G-A
• chr13-84815953-G-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 0.213 in 151,750 control chromosomes in the GnomAD database, including 4,234 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 (4234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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: 0.213 AC: 32287 AN: 151632 Hom.: 4223 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0501

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.213 AC: 32329 AN: 151750 Hom.: 4234 Cov.: 32 AF XY: 0.207 AC XY: 15318 AN XY: 74138

African (AFR) AF: 0.367 AC: 15210 AN: 41408

American (AMR) AF: 0.142 AC: 2162 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3464

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0497 AC: 239 AN: 4810

European-Finnish (FIN) AF: 0.156 AC: 1637 AN: 10520

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11834 AN: 67846

Other (OTH) AF: 0.209 AC: 440 AN: 2110

Alfa AF: 0.0943 Hom.: 127

Bravo AF: 0.220

Asia WGS AF: 0.0480 AC: 166 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.075
DANN	Benign	0.61
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1949891; hg19: chr13-85390088;