2-67491158-C-T

Variant names:

• chr2-67491158-C-T
• rs7584345

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.643 in 152,082 control chromosomes in the GnomAD database, including 31,974 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 0.64 (31974 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 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: 0.644 AC: 97791 AN: 151962 Hom.: 31961 Cov.: 34

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.643 AC: 97844 AN: 152082 Hom.: 31974 Cov.: 34 AF XY: 0.639 AC XY: 47494 AN XY: 74338

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.654

Alfa AF: 0.684 Hom.: 81958

Bravo AF: 0.624

Asia WGS AF: 0.636 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7584345; hg19: chr2-67718290;