rs7601770

Positions:

• chr2-62431121-T-C

Variant summary

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

The ENST00000689590.1(ENSG00000228541):​n.164-32718T>C 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 0.324 in 151,840 control chromosomes in the GnomAD database, including 8,489 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 0.32 (8489 hom., cov: 30)
• Consequence: ENST00000689590.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374764	XR_002959390.2	n.293+68T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000689590.1	n.164-32718T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49207 AN: 151722 Hom.: 8492 Cov.: 30

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.324 AC: 49219 AN: 151840 Hom.: 8489 Cov.: 30 AF XY: 0.314 AC XY: 23285 AN XY: 74194

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0289

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.308

Alfa AF: 0.342 Hom.: 1464

Bravo AF: 0.315

Asia WGS AF: 0.109 AC: 381 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	0.16
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7601770; hg19: chr2-62658256;