rs1341758

Positions:

• chr6-26200290-G-A
• chr6-26200290-G-C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+76119G>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 0.0492 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: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

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 (SAS) allele frequency at 95% confidence interval = 0.0646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000707189.1	n.999+76119G>A		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1000+42169G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.0530

Gnomad4 AMR exome AF: 0.0580

Gnomad4 ASJ exome AF: 0.0432

Gnomad4 EAS exome AF: 0.0294

Gnomad4 SAS exome AF: 0.0643

Gnomad4 FIN exome AF: 0.0449

Gnomad4 NFE exome AF: 0.0512

Gnomad4 OTH exome AF: 0.0528

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

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.0565

Gnomad4 SAS AF: 0.0708

Gnomad4 FIN AF: 0.0415

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0574

Alfa AF: 0.0402 Hom.: 81

Bravo AF: 0.0492

Asia WGS AF: 0.0610 AC: 213 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	2.0
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341758; hg19: chr6-26200518;