2-41723813-A-G

Position:

• chr2-41723813-A-G

Variant summary

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

The ENST00000660664.1(ENSG00000287145):​n.110-874A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,070 control chromosomes in the GnomAD database, including 6,679 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 0.28 (6679 hom., cov: 32)
• Consequence: ENST00000660664.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660664.1	n.110-874A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42992 AN: 151952 Hom.: 6669 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.283 AC: 43033 AN: 152070 Hom.: 6679 Cov.: 32 AF XY: 0.281 AC XY: 20852 AN XY: 74338

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.219

Alfa AF: 0.292 Hom.: 1311

Bravo AF: 0.277

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11692045; hg19: chr2-41950953;