rs786100

Variant names:

• chr6-122241607-G-T
• rs786100
• ENST00000837532.1:n.342-27750C>A

Variant summary

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

The ENST00000837532.1(ENSG00000308965):​n.342-27750C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,636 control chromosomes in the GnomAD database, including 4,796 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 0.23 (4796 hom., cov: 32)
• Consequence: ENSG00000308965 ENST00000837532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 1 publications found

Genes affected

ENSG00000308965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 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
ENSG00000308965	ENST00000837532.1	n.342-27750C>A		intron_variant	Intron 2 of 2
ENSG00000308965	ENST00000837533.1	n.226-17447C>A		intron_variant	Intron 2 of 3
ENSG00000308965	ENST00000837534.1	n.376-17447C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35552 AN: 151514 Hom.: 4795 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.234 AC: 35545 AN: 151636 Hom.: 4796 Cov.: 32 AF XY: 0.229 AC XY: 16989 AN XY: 74134

African (AFR) AF: 0.107 AC: 4434 AN: 41458

American (AMR) AF: 0.223 AC: 3395 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3462

East Asian (EAS) AF: 0.350 AC: 1806 AN: 5164

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4820

European-Finnish (FIN) AF: 0.215 AC: 2250 AN: 10474

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20443 AN: 67740

Other (OTH) AF: 0.247 AC: 518 AN: 2096

Alfa AF: 0.257 Hom.: 709

Bravo AF: 0.234

Asia WGS AF: 0.251 AC: 872 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs786100; hg19: chr6-122562753;