rs1954971

Variant names:

• chr18-30799277-T-C
• rs1954971

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 0.364 in 152,102 control chromosomes in the GnomAD database, including 10,084 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 0.36 (10084 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.364 AC: 55253 AN: 151984 Hom.: 10081 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.364 AC: 55293 AN: 152102 Hom.: 10084 Cov.: 33 AF XY: 0.365 AC XY: 27108 AN XY: 74336

African (AFR) AF: 0.360 AC: 14947 AN: 41498

American (AMR) AF: 0.377 AC: 5756 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3468

East Asian (EAS) AF: 0.419 AC: 2162 AN: 5166

South Asian (SAS) AF: 0.343 AC: 1655 AN: 4828

European-Finnish (FIN) AF: 0.399 AC: 4216 AN: 10576

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24743 AN: 67978

Other (OTH) AF: 0.356 AC: 750 AN: 2106

Alfa AF: 0.355 Hom.: 1230

Bravo AF: 0.365

Asia WGS AF: 0.401 AC: 1390 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.72
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs1954971; hg19: chr18-28379243;