7-9855925-G-A

Variant names:

• chr7-9855925-G-A
• rs1117702
• ENST00000731005.1:n.278+10865C>T

Variant summary

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

The ENST00000731005.1(ENSG00000295572):​n.278+10865C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,010 control chromosomes in the GnomAD database, including 3,825 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 0.22 (3825 hom., cov: 32)
• Consequence: ENSG00000295572 ENST00000731005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 1 publications found

Genes affected

ENSG00000295572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731005.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295572	ENST00000731005.1		n.278+10865C>T		intron	N/A
	ENSG00000295572	ENST00000731006.1		n.169+10865C>T		intron	N/A
	ENSG00000295572	ENST00000731007.1		n.241+10865C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32958 AN: 151890 Hom.: 3826 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.217 AC: 32960 AN: 152010 Hom.: 3825 Cov.: 32 AF XY: 0.218 AC XY: 16210 AN XY: 74302

African (AFR) AF: 0.144 AC: 5981 AN: 41486

American (AMR) AF: 0.193 AC: 2947 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1069 AN: 5140

South Asian (SAS) AF: 0.315 AC: 1520 AN: 4826

European-Finnish (FIN) AF: 0.263 AC: 2777 AN: 10548

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17185 AN: 67972

Other (OTH) AF: 0.199 AC: 421 AN: 2114

Alfa AF: 0.185 Hom.: 991

Bravo AF: 0.203

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.84
PhyloP100		-0.45

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: rs1117702;

hg19: chr7-9895554;