rs10488401

Positions:

• chr7-136140776-A-G
• chr7-136140776-A-T

Variant summary

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

The ENST00000668062.1(ENSG00000232053):​n.114+47740A>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 0.622 in 152,092 control chromosomes in the GnomAD database, including 32,253 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 0.62 (32253 hom., cov: 33)
• Consequence: ENST00000668062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375523	XR_007060545.1	n.365-36476A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668062.1	n.114+47740A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94497 AN: 151974 Hom.: 32199 Cov.: 33

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.622 AC: 94591 AN: 152092 Hom.: 32253 Cov.: 33 AF XY: 0.609 AC XY: 45266 AN XY: 74356

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.586

Alfa AF: 0.584 Hom.: 5270

Bravo AF: 0.625

Asia WGS AF: 0.338 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488401; hg19: chr7-135825524;