rs41440

Variant names:

• chr7-86145233-A-G
• rs41440
• ENST00000757672.1:n.145-26171T>C

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.145-26171T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,006 control chromosomes in the GnomAD database, including 5,555 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 0.26 (5555 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 3 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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
ENSG00000298738	ENST00000757672.1	n.145-26171T>C		intron_variant	Intron 2 of 3
ENSG00000298738	ENST00000757673.1	n.143+39176T>C		intron_variant	Intron 2 of 2
ENSG00000298738	ENST00000757674.1	n.144-14206T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39587 AN: 151888 Hom.: 5554 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.260 AC: 39596 AN: 152006 Hom.: 5555 Cov.: 32 AF XY: 0.261 AC XY: 19353 AN XY: 74280

African (AFR) AF: 0.297 AC: 12307 AN: 41456

American (AMR) AF: 0.201 AC: 3071 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3468

East Asian (EAS) AF: 0.122 AC: 633 AN: 5182

South Asian (SAS) AF: 0.117 AC: 564 AN: 4830

European-Finnish (FIN) AF: 0.384 AC: 4065 AN: 10574

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17442 AN: 67932

Other (OTH) AF: 0.227 AC: 477 AN: 2104

Alfa AF: 0.248 Hom.: 2450

Bravo AF: 0.251

Asia WGS AF: 0.137 AC: 477 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.42
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs41440; hg19: chr7-85774549;