rs76387818

Variant names:

• chr1-97073844-G-A
• rs76387818

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.022 in 152,206 control chromosomes in the GnomAD database, including 44 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 0.022 (44 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.022 (3344/152206) while in subpopulation NFE AF= 0.0324 (2202/67990). AF 95% confidence interval is 0.0313. There are 44 homozygotes in gnomad4. There are 1551 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 44 gene

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: 0.0220 AC: 3347 AN: 152088 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00975

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00518

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0220 AC: 3344 AN: 152206 Hom.: 44 Cov.: 32 AF XY: 0.0208 AC XY: 1551 AN XY: 74406

Gnomad4 AFR AF: 0.00970

Gnomad4 AMR AF: 0.0218

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00539

Gnomad4 FIN AF: 0.0228

Gnomad4 NFE AF: 0.0324

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0243 Hom.: 8

Bravo AF: 0.0218

Asia WGS AF: 0.00549 AC: 19 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	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76387818; hg19: chr1-97539400;