ENST00000707189.1:n.999+76119G>A

Variant names:

• chr6-26200290-G-A
• rs1341758
• ENST00000707189.1:n.999+76119G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707189.1(ENSG00000291336):​n.999+76119G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 249,166 control chromosomes in the GnomAD database, including 317 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 0.048 (206 hom., cov: 33)
  • Exomes 𝑓: 0.051 (111 hom.)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 9 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0646 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707189.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291336	ENST00000707189.1		n.999+76119G>A		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1000+42169G>A		intron	N/A
	ENSG00000301014	ENST00000775520.1		n.135-2128G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0481 AC: 7320 AN: 152212 Hom.: 207 Cov.: 33

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.0561

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0590

GnomAD4 exome AF: 0.0510 AC: 4935 AN: 96836 Hom.: 111 Cov.: 0 AF XY: 0.0511 AC XY: 2553 AN XY: 49914

African (AFR) AF: 0.0530 AC: 145 AN: 2738

American (AMR) AF: 0.0580 AC: 288 AN: 4962

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 145 AN: 3354

East Asian (EAS) AF: 0.0294 AC: 196 AN: 6678

South Asian (SAS) AF: 0.0643 AC: 496 AN: 7710

European-Finnish (FIN) AF: 0.0449 AC: 193 AN: 4300

Middle Eastern (MID) AF: 0.104 AC: 47 AN: 452

European-Non Finnish (NFE) AF: 0.0512 AC: 3102 AN: 60530

Other (OTH) AF: 0.0528 AC: 323 AN: 6112

GnomAD4 genome AF: 0.0480 AC: 7317 AN: 152330 Hom.: 206 Cov.: 33 AF XY: 0.0483 AC XY: 3596 AN XY: 74482

African (AFR) AF: 0.0473 AC: 1965 AN: 41574

American (AMR) AF: 0.0602 AC: 921 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3470

East Asian (EAS) AF: 0.0565 AC: 293 AN: 5190

South Asian (SAS) AF: 0.0708 AC: 342 AN: 4830

European-Finnish (FIN) AF: 0.0415 AC: 440 AN: 10612

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3092 AN: 68038

Other (OTH) AF: 0.0574 AC: 121 AN: 2108

Alfa AF: 0.0448 Hom.: 168

Bravo AF: 0.0492

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		-0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1341758; hg19: chr6-26200518;