rs7846876

Variant names:

• chr9-13832882-G-C
• rs7846876
• ENST00000664438.1:n.163-3431G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000664438.1(ENSG00000226197):​n.163-3431G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00217 in 152,216 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0022 (0 hom., cov: 32)
• Consequence: ENSG00000226197 ENST00000664438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 2 publications found

Genes affected

ENSG00000226197 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929507	XR_001746620.2	n.898-15714C>G		intron_variant	Intron 8 of 8
LOC101929507	XR_001746621.2	n.830-15714C>G		intron_variant	Intron 7 of 7
LOC124902326	XR_007061894.1	n.40+2963G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226197	ENST00000664438.1	n.163-3431G>C		intron_variant	Intron 2 of 2
ENSG00000289185	ENST00000741129.1	n.1092-24461C>G		intron_variant	Intron 9 of 10
ENSG00000289185	ENST00000741130.1	n.1482+49017C>G		intron_variant	Intron 12 of 13

Frequencies

GnomAD3 genomes AF: 0.00215 AC: 327 AN: 152098 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00287

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

GnomAD4 genome AF: 0.00217 AC: 330 AN: 152216 Hom.: 0 Cov.: 32 AF XY: 0.00206 AC XY: 153 AN XY: 74420

African (AFR) AF: 0.00729 AC: 303 AN: 41550

American (AMR) AF: 0.000655 AC: 10 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4814

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10606

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 68014

Other (OTH) AF: 0.00284 AC: 6 AN: 2116

Alfa AF: 0.00160 Hom.: 1

Bravo AF: 0.00235

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7846876; hg19: chr9-13832881;