1-4399629-T-C

Variant names:

• chr1-4399629-T-C
• rs6679220

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 0.407 in 152,144 control chromosomes in the GnomAD database, including 13,213 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 0.41 (13213 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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: 0.407 AC: 61854 AN: 152026 Hom.: 13209 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.407 AC: 61881 AN: 152144 Hom.: 13213 Cov.: 33 AF XY: 0.400 AC XY: 29727 AN XY: 74392

African (AFR) AF: 0.374 AC: 15530 AN: 41504

American (AMR) AF: 0.324 AC: 4948 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1581 AN: 3472

East Asian (EAS) AF: 0.0982 AC: 507 AN: 5164

South Asian (SAS) AF: 0.286 AC: 1379 AN: 4820

European-Finnish (FIN) AF: 0.422 AC: 4470 AN: 10596

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 31988 AN: 67986

Other (OTH) AF: 0.412 AC: 870 AN: 2110

Alfa AF: 0.442 Hom.: 19718

Bravo AF: 0.398

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.042
DANN	Benign	0.13
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6679220; hg19: chr1-4459689;