chr6-98430936-A-G

Variant names:

• chr6-98430936-A-G
• rs2047179
• ENST00000847792.1:n.648-19746A>G

Variant summary

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

The ENST00000847792.1(ENSG00000271860):​n.648-19746A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,942 control chromosomes in the GnomAD database, including 6,908 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 0.30 (6908 hom., cov: 32)
• Consequence: ENSG00000271860 ENST00000847792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 1 publications found

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 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
ENSG00000271860	ENST00000847792.1	n.648-19746A>G		intron_variant	Intron 6 of 7
ENSG00000271860	ENST00000847793.1	n.612-19746A>G		intron_variant	Intron 6 of 9
ENSG00000271860	ENST00000847794.1	n.461-31387A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45625 AN: 151822 Hom.: 6904 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.301 AC: 45663 AN: 151942 Hom.: 6908 Cov.: 32 AF XY: 0.303 AC XY: 22470 AN XY: 74246

African (AFR) AF: 0.265 AC: 11001 AN: 41472

American (AMR) AF: 0.282 AC: 4295 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1295 AN: 3464

East Asian (EAS) AF: 0.257 AC: 1326 AN: 5160

South Asian (SAS) AF: 0.244 AC: 1172 AN: 4812

European-Finnish (FIN) AF: 0.340 AC: 3589 AN: 10548

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22055 AN: 67926

Other (OTH) AF: 0.302 AC: 637 AN: 2110

Alfa AF: 0.314 Hom.: 1299

Bravo AF: 0.294

Asia WGS AF: 0.213 AC: 743 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs2047179; hg19: chr6-98878812; COSMIC: COSV69415044;