chr1-218240701-T-G

Variant names:

• chr1-218240701-T-G
• rs6663771

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 0.654 in 152,068 control chromosomes in the GnomAD database, including 33,100 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 0.65 (33100 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.654 AC: 99378 AN: 151950 Hom.: 33042 Cov.: 33

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.654 AC: 99491 AN: 152068 Hom.: 33100 Cov.: 33 AF XY: 0.657 AC XY: 48862 AN XY: 74342

African (AFR) AF: 0.711 AC: 29492 AN: 41488

American (AMR) AF: 0.741 AC: 11324 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3466

East Asian (EAS) AF: 0.912 AC: 4718 AN: 5174

South Asian (SAS) AF: 0.765 AC: 3687 AN: 4820

European-Finnish (FIN) AF: 0.561 AC: 5935 AN: 10574

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39808 AN: 67956

Other (OTH) AF: 0.678 AC: 1431 AN: 2110

Alfa AF: 0.615 Hom.: 14664

Bravo AF: 0.675

Asia WGS AF: 0.817 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.049
DANN	Benign	0.52
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6663771; hg19: chr1-218414043; COSMIC: COSV60028052;