7-128217838-G-T

Variant summary

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

The ENST00000710955.1(ENSG00000292309):n.836-6195G>T 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 0.345 in 152,110 control chromosomes in the GnomAD database, including 10,216 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 0.35 (10216 hom., cov: 33)
• Consequence: ENST00000710955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901744	XR_007060516.1	n.781-6195G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710955.1	n.836-6195G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52492 AN: 151992 Hom.: 10213 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.345 AC: 52510 AN: 152110 Hom.: 10216 Cov.: 33 AF XY: 0.348 AC XY: 25890 AN XY: 74338

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.373

Alfa AF: 0.391 Hom.: 24389

Bravo AF: 0.331

Asia WGS AF: 0.489 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	12
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2167289; hg19: chr7-127857891;