1-6704603-T-C

Variant names:

• chr1-6704603-T-C
• rs278021

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 0.786 in 151,932 control chromosomes in the GnomAD database, including 47,407 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 0.79 (47407 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.786 AC: 119375 AN: 151810 Hom.: 47358 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.798

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.786 AC: 119482 AN: 151932 Hom.: 47407 Cov.: 31 AF XY: 0.789 AC XY: 58542 AN XY: 74242

African (AFR) AF: 0.799 AC: 33107 AN: 41434

American (AMR) AF: 0.680 AC: 10384 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5162 AN: 5186

South Asian (SAS) AF: 0.886 AC: 4267 AN: 4814

European-Finnish (FIN) AF: 0.745 AC: 7844 AN: 10526

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.786 AC: 53404 AN: 67932

Other (OTH) AF: 0.788 AC: 1661 AN: 2108

Alfa AF: 0.791 Hom.: 23652

Bravo AF: 0.778

Asia WGS AF: 0.924 AC: 3214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.46
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs278021; hg19: chr1-6764663;