chr7-150897578-T-G

Variant names:

• chr7-150897578-T-G
• rs885684
• ENST00000726373.1:n.221+3817A>C

Variant summary

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

The ENST00000726373.1(ENSG00000289052):​n.221+3817A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,852 control chromosomes in the GnomAD database, including 9,430 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 0.35 (9430 hom., cov: 31)
• Consequence: ENSG00000289052 ENST00000726373.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 2 publications found

Genes affected

ENSG00000289052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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
ENSG00000289052	ENST00000726373.1	n.221+3817A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52626 AN: 151734 Hom.: 9421 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.347 AC: 52675 AN: 151852 Hom.: 9430 Cov.: 31 AF XY: 0.340 AC XY: 25250 AN XY: 74212

African (AFR) AF: 0.411 AC: 17022 AN: 41378

American (AMR) AF: 0.287 AC: 4386 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 989 AN: 3464

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5164

South Asian (SAS) AF: 0.301 AC: 1446 AN: 4804

European-Finnish (FIN) AF: 0.266 AC: 2812 AN: 10552

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23820 AN: 67914

Other (OTH) AF: 0.346 AC: 727 AN: 2102

Alfa AF: 0.241 Hom.: 574

Bravo AF: 0.349

Asia WGS AF: 0.253 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.41
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs885684; hg19: chr7-150594666;