chr7-9855925-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375147	XR_927026.2	n.209+10865C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295572	ENST00000731005.1	n.278+10865C>T		intron_variant	Intron 2 of 3
ENSG00000295572	ENST00000731006.1	n.169+10865C>T		intron_variant	Intron 2 of 4
ENSG00000295572	ENST00000731007.1	n.241+10865C>T		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1117702; hg19: chr7-9895554;