10-86755315-T-C

Variant names:

• chr10-86755315-T-C
• rs3905377
• ENST00000608826.2:n.1072A>G

Variant summary

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

The ENST00000608826.2(ENSG00000272631):​n.1072A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,130 control chromosomes in the GnomAD database, including 7,675 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 0.29 (7673 hom., cov: 33)
  • Exomes 𝑓: 0.70 (2 hom.)
• Consequence: ENSG00000272631 ENST00000608826.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 9 publications found

Genes affected

ENSG00000272631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272631	ENST00000608826.2	n.1072A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000272631	ENST00000740897.1	n.526+436A>G		intron_variant	Intron 1 of 1
ENSG00000272631	ENST00000740898.1	n.230+726A>G		intron_variant	Intron 1 of 1
ENSG00000272631	ENST00000740899.1	n.201+436A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44079 AN: 152002 Hom.: 7672 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.290 AC: 44087 AN: 152120 Hom.: 7673 Cov.: 33 AF XY: 0.297 AC XY: 22057 AN XY: 74344

African (AFR) AF: 0.123 AC: 5100 AN: 41530

American (AMR) AF: 0.325 AC: 4972 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3468

East Asian (EAS) AF: 0.697 AC: 3596 AN: 5162

South Asian (SAS) AF: 0.353 AC: 1697 AN: 4808

European-Finnish (FIN) AF: 0.390 AC: 4119 AN: 10570

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22363 AN: 67976

Other (OTH) AF: 0.292 AC: 618 AN: 2114

Alfa AF: 0.323 Hom.: 31903

Bravo AF: 0.279

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.0
DANN	Benign	0.73
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3905377; hg19: chr10-88515072;