ENST00000663105.1:n.78T>A

Variant names:

• chr7-157502244-T-A
• rs10227331
• ENST00000663105.1:n.78T>A

Variant summary

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

The ENST00000663105.1(ENSG00000223872):​n.78T>A 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 0.434 in 151,962 control chromosomes in the GnomAD database, including 14,545 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 0.43 (14545 hom., cov: 32)
• Consequence: ENSG00000223872 ENST00000663105.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

Genes affected

ENSG00000223872 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375610	NR_187970.1	n.169T>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105375610	NR_187971.1	n.169T>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105375610	NR_187969.1	n.110+729T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223872	ENST00000663105.1	n.78T>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000223872	ENST00000665840.1	n.115T>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000223872	ENST00000670480.1	n.86T>A		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65989 AN: 151844 Hom.: 14548 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.434 AC: 66015 AN: 151962 Hom.: 14545 Cov.: 32 AF XY: 0.437 AC XY: 32438 AN XY: 74264

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.435

Alfa AF: 0.439 Hom.: 7885

Bravo AF: 0.417

Asia WGS AF: 0.417 AC: 1450 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	1.1
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10227331; hg19: chr7-157294938;