rs1949891

Positions:

• chr13-84815953-G-A
• chr13-84815953-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.209

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1949891; hg19: chr13-85390088;