rs6677984

Variant names:

• chr1-4270227-A-G
• rs6677984

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 0.524 in 152,038 control chromosomes in the GnomAD database, including 21,161 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 0.52 (21161 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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: 0.524 AC: 79542 AN: 151922 Hom.: 21143 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.524 AC: 79610 AN: 152038 Hom.: 21161 Cov.: 33 AF XY: 0.521 AC XY: 38702 AN XY: 74350

African (AFR) AF: 0.574 AC: 23778 AN: 41452

American (AMR) AF: 0.559 AC: 8545 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5162

South Asian (SAS) AF: 0.528 AC: 2546 AN: 4820

European-Finnish (FIN) AF: 0.495 AC: 5230 AN: 10576

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34955 AN: 67958

Other (OTH) AF: 0.490 AC: 1032 AN: 2108

Alfa AF: 0.504 Hom.: 30573

Bravo AF: 0.523

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.47
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs6677984; hg19: chr1-4330287;