rs7748777

chr6-41166068-G-A

Variant summary

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

The ENST00000702590.1(ENSG00000290034):n.364+10505G>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 0.58 in 152,044 control chromosomes in the GnomAD database, including 28,131 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 0.58 (28131 hom., cov: 33)
• Consequence: ENST00000702590.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 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
	ENST00000702590.1	n.364+10505G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88137 AN: 151928 Hom.: 28074 Cov.: 33

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.580 AC: 88247 AN: 152044 Hom.: 28131 Cov.: 33 AF XY: 0.575 AC XY: 42716 AN XY: 74314

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.560

Alfa AF: 0.480 Hom.: 25182

Bravo AF: 0.601

Asia WGS AF: 0.557 AC: 1933 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.36
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7748777; hg19: chr6-41133806;