chr6-20250595-G-A

Variant names:

• chr6-20250595-G-A
• rs9465673
• ENST00000449143.2:n.91+38418G>A

Variant summary

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

The ENST00000449143.2(ENSG00000227803):​n.91+38418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,112 control chromosomes in the GnomAD database, including 3,039 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 0.20 (3039 hom., cov: 32)
• Consequence: ENSG00000227803 ENST00000449143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

Genes affected

ENSG00000227803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449143.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227803	ENST00000449143.2	TSL:3	n.91+38418G>A		intron	N/A
	ENSG00000227803	ENST00000718207.1		n.81-15128G>A		intron	N/A
	ENSG00000227803	ENST00000718208.1		n.59-29456G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29718 AN: 151994 Hom.: 3036 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0919

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.195 AC: 29726 AN: 152112 Hom.: 3039 Cov.: 32 AF XY: 0.201 AC XY: 14909 AN XY: 74358

African (AFR) AF: 0.171 AC: 7086 AN: 41498

American (AMR) AF: 0.154 AC: 2355 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3470

East Asian (EAS) AF: 0.0919 AC: 476 AN: 5180

South Asian (SAS) AF: 0.275 AC: 1326 AN: 4820

European-Finnish (FIN) AF: 0.287 AC: 3029 AN: 10560

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14099 AN: 67990

Other (OTH) AF: 0.191 AC: 402 AN: 2108

Alfa AF: 0.202 Hom.: 5261

Bravo AF: 0.180

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9465673; hg19: chr6-20250826;