6-32898220-T-C

Variant names:

• chr6-32898220-T-C
• rs241404
• ENST00000685247.3:n.884-2700T>C

Variant summary

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

The NR_037177.1(LOC100294145):​n.852-2700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,984 control chromosomes in the GnomAD database, including 13,457 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 0.42 (13457 hom., cov: 31)
• Consequence: LOC100294145 NR_037177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 35 publications found

Genes affected

ENSG00000289047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_037177.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100294145	NR_037177.1		n.852-2700T>C		intron	N/A
	LOC100294145	NR_037178.1		n.753-2700T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289047	ENST00000685247.3		n.884-2700T>C		intron	N/A
	ENSG00000289047	ENST00000701517.2		n.684-2700T>C		intron	N/A
	ENSG00000289047	ENST00000753208.1		n.521-2700T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63262 AN: 151866 Hom.: 13458 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.416 AC: 63281 AN: 151984 Hom.: 13457 Cov.: 31 AF XY: 0.411 AC XY: 30544 AN XY: 74292

African (AFR) AF: 0.456 AC: 18908 AN: 41430

American (AMR) AF: 0.352 AC: 5381 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2122 AN: 5174

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4822

European-Finnish (FIN) AF: 0.400 AC: 4224 AN: 10548

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28531 AN: 67948

Other (OTH) AF: 0.409 AC: 862 AN: 2110

Alfa AF: 0.423 Hom.: 40310

Bravo AF: 0.415

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.1
DANN	Benign	0.89
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs241404; hg19: chr6-32865997;