chr1-223464379-G-T

Variant names:

• chr1-223464379-G-T
• rs6671793

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 0.385 in 151,994 control chromosomes in the GnomAD database, including 11,559 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 0.38 (11559 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.385 AC: 58413 AN: 151876 Hom.: 11532 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.385 AC: 58489 AN: 151994 Hom.: 11559 Cov.: 32 AF XY: 0.384 AC XY: 28511 AN XY: 74298

African (AFR) AF: 0.467 AC: 19348 AN: 41446

American (AMR) AF: 0.422 AC: 6439 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2704 AN: 5170

South Asian (SAS) AF: 0.253 AC: 1215 AN: 4810

European-Finnish (FIN) AF: 0.321 AC: 3384 AN: 10552

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23068 AN: 67980

Other (OTH) AF: 0.360 AC: 759 AN: 2108

Alfa AF: 0.340 Hom.: 4741

Bravo AF: 0.398

Asia WGS AF: 0.370 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.047
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6671793; hg19: chr1-223637721;