6-25481763-G-A

Variant names:

• chr6-25481763-G-A
• rs10498726
• NM_017640.6:c.875-494G>A

Variant summary

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

The NM_017640.6(CARMIL1):​c.875-494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,138 control chromosomes in the GnomAD database, including 2,156 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 0.15 (2156 hom., cov: 32)
• Consequence: CARMIL1 NM_017640.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507
• Publications: 3 publications found

Genes affected

CARMIL1 (HGNC:21581): (capping protein regulator and myosin 1 linker 1) Involved in several processes, including actin filament network formation; plasma membrane bounded cell projection organization; and positive regulation of cellular component organization. Located in several cellular components, including lamellipodium; macropinosome; and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARMIL1	NM_017640.6	c.875-494G>A		intron_variant	Intron 11 of 36	ENST00000329474.7	NP_060110.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARMIL1	ENST00000329474.7	c.875-494G>A		intron_variant	Intron 11 of 36	1	NM_017640.6	ENSP00000331983.6
CARMIL1	ENST00000700669.1	c.875-494G>A		intron_variant	Intron 11 of 36			ENSP00000515137.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23224 AN: 152020 Hom.: 2152 Cov.: 32

Gnomad AFR AF: 0.0480

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.153 AC: 23248 AN: 152138 Hom.: 2156 Cov.: 32 AF XY: 0.155 AC XY: 11506 AN XY: 74390

African (AFR) AF: 0.0480 AC: 1992 AN: 41522

American (AMR) AF: 0.198 AC: 3036 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.172 AC: 892 AN: 5172

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2004 AN: 10566

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 12979 AN: 67984

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.182 Hom.: 8513

Bravo AF: 0.150

Asia WGS AF: 0.211 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.64
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10498726; hg19: chr6-25481991;