rs1971376

Variant names:

• chr8-23671146-A-G
• rs1971376
• ENST00000835200.1:n.475+2396A>G

Variant summary

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

The ENST00000835200.1(ENSG00000308589):​n.475+2396A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,102 control chromosomes in the GnomAD database, including 6,005 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 0.28 (6005 hom., cov: 32)
• Consequence: ENSG00000308589 ENST00000835200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 6 publications found

Genes affected

ENSG00000308589 (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 (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986930	XR_001745842.2	n.1312+2396A>G		intron_variant	Intron 3 of 4
LOC107986930	XR_001745841.2	n.*229A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308589	ENST00000835200.1	n.475+2396A>G		intron_variant	Intron 4 of 4
ENSG00000308589	ENST00000835201.1	n.1097+2396A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42136 AN: 151986 Hom.: 6003 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.277 AC: 42165 AN: 152102 Hom.: 6005 Cov.: 32 AF XY: 0.286 AC XY: 21232 AN XY: 74348

African (AFR) AF: 0.277 AC: 11509 AN: 41480

American (AMR) AF: 0.304 AC: 4645 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1450 AN: 5178

South Asian (SAS) AF: 0.334 AC: 1610 AN: 4824

European-Finnish (FIN) AF: 0.379 AC: 4008 AN: 10564

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16993 AN: 67992

Other (OTH) AF: 0.276 AC: 583 AN: 2116

Alfa AF: 0.253 Hom.: 2181

Bravo AF: 0.270

Asia WGS AF: 0.326 AC: 1134 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	2.0
DANN	Benign	0.60
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1971376; hg19: chr8-23528659;