rs2250603

chr7-136286559-G-A

Variant summary

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

The ENST00000668062.1(ENSG00000232053):n.337-42423G>A 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 0.144 in 152,074 control chromosomes in the GnomAD database, including 1,898 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 0.14 (1898 hom., cov: 32)
• Consequence: ENST00000668062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375523	XR_007060545.1	n.749-42423G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668062.1	n.337-42423G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21888 AN: 151956 Hom.: 1885 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.144 AC: 21913 AN: 152074 Hom.: 1898 Cov.: 32 AF XY: 0.145 AC XY: 10746 AN XY: 74358

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.0840

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.150

Alfa AF: 0.134 Hom.: 299

Bravo AF: 0.154

Asia WGS AF: 0.205 AC: 711 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.6
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2250603; hg19: chr7-135971307;