1-236096271-T-C

Variant names:

• chr1-236096271-T-C
• rs966302

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 0.552 in 152,046 control chromosomes in the GnomAD database, including 23,693 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 0.55 (23693 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 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: 0.552 AC: 83841 AN: 151928 Hom.: 23650 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.552 AC: 83945 AN: 152046 Hom.: 23693 Cov.: 33 AF XY: 0.553 AC XY: 41074 AN XY: 74318

African (AFR) AF: 0.667 AC: 27658 AN: 41462

American (AMR) AF: 0.551 AC: 8415 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3373 AN: 5182

South Asian (SAS) AF: 0.568 AC: 2736 AN: 4818

European-Finnish (FIN) AF: 0.473 AC: 4996 AN: 10552

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33726 AN: 67968

Other (OTH) AF: 0.534 AC: 1127 AN: 2112

Alfa AF: 0.508 Hom.: 32922

Bravo AF: 0.561

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs966302; hg19: chr1-236259571;