7-24197136-C-T

Variant names:

• chr7-24197136-C-T
• rs156293
• ENST00000439839.1:n.160-107G>A

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.320-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,732 control chromosomes in the GnomAD database, including 9,656 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 0.33 (9656 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 4 publications found

Genes affected

ENSG00000228944 (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 = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718234.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228944	ENST00000439839.1	TSL:5	n.160-107G>A		intron	N/A
	ENSG00000228944	ENST00000718234.1		n.320-107G>A		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.342-107G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50573 AN: 151614 Hom.: 9645 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.312

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.334 AC: 50615 AN: 151732 Hom.: 9656 Cov.: 31 AF XY: 0.339 AC XY: 25138 AN XY: 74128

African (AFR) AF: 0.507 AC: 20957 AN: 41336

American (AMR) AF: 0.350 AC: 5336 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 657 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2453 AN: 5138

South Asian (SAS) AF: 0.419 AC: 2003 AN: 4784

European-Finnish (FIN) AF: 0.255 AC: 2691 AN: 10538

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15660 AN: 67928

Other (OTH) AF: 0.309 AC: 649 AN: 2102

Alfa AF: 0.297 Hom.: 1292

Bravo AF: 0.349

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.066

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs156293;

hg19: chr7-24236755;