ENST00000663105.1:n.78T>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000223872 (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 (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663105.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375610	NR_187970.1		n.169T>A		non_coding_transcript_exon	Exon 1 of 3
	LOC105375610	NR_187971.1		n.169T>A		non_coding_transcript_exon	Exon 1 of 3
	LOC105375610	NR_187969.1		n.110+729T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223872	ENST00000663105.1		n.78T>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000223872	ENST00000665840.1		n.115T>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000223872	ENST00000670480.1		n.86T>A		non_coding_transcript_exon	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

African (AFR) AF: 0.363 AC: 15040 AN: 41434

American (AMR) AF: 0.406 AC: 6204 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2211 AN: 5166

South Asian (SAS) AF: 0.374 AC: 1796 AN: 4802

European-Finnish (FIN) AF: 0.569 AC: 5998 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31593 AN: 67964

Other (OTH) AF: 0.435 AC: 918 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.86
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10227331;

hg19: chr7-157294938;