rs2202749

Positions:

• chr8-80362103-A-G
• chr8-80362103-A-T

Variant summary

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

The ENST00000656157.1(ENSG00000253238):​n.273+73101A>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 0.612 in 150,240 control chromosomes in the GnomAD database, including 28,538 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 0.61 (28538 hom., cov: 26)
• Consequence: ENST00000656157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 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
	ENST00000656157.1	n.273+73101A>G		intron_variant, non_coding_transcript_variant
	ENST00000644465.1	n.253+73101A>G		intron_variant, non_coding_transcript_variant
	ENST00000656811.1	n.252-40633A>G		intron_variant, non_coding_transcript_variant
	ENST00000662273.1	n.370+73101A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.613 AC: 91970 AN: 150132 Hom.: 28525 Cov.: 26

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.612 AC: 92021 AN: 150240 Hom.: 28538 Cov.: 26 AF XY: 0.611 AC XY: 44658 AN XY: 73148

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.621

Alfa AF: 0.620 Hom.: 3506

Bravo AF: 0.597

Asia WGS AF: 0.518 AC: 1797 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2202749; hg19: chr8-81274338;