chr6-37797201-C-G

Variant names:

• chr6-37797201-C-G
• rs7750445
• ENST00000810126.1:n.438-4415C>G

Variant summary

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

The ENST00000810126.1(ENSG00000305289):​n.438-4415C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,028 control chromosomes in the GnomAD database, including 2,017 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 0.16 (2017 hom., cov: 31)
• Consequence: ENSG00000305289 ENST00000810126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 3 publications found

Genes affected

ENSG00000305289 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 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
ENSG00000305289	ENST00000810126.1	n.438-4415C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24516 AN: 151910 Hom.: 2017 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.161 AC: 24521 AN: 152028 Hom.: 2017 Cov.: 31 AF XY: 0.159 AC XY: 11818 AN XY: 74284

African (AFR) AF: 0.141 AC: 5865 AN: 41510

American (AMR) AF: 0.142 AC: 2169 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3470

East Asian (EAS) AF: 0.0487 AC: 250 AN: 5136

South Asian (SAS) AF: 0.155 AC: 746 AN: 4812

European-Finnish (FIN) AF: 0.160 AC: 1694 AN: 10566

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12280 AN: 67954

Other (OTH) AF: 0.158 AC: 333 AN: 2112

Alfa AF: 0.0869 Hom.: 126

Bravo AF: 0.157

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7750445; hg19: chr6-37764977;